Add additional test profiles, needing the github secrets

nf-core · Apr 26, 2024 · 643061a · 643061a
1 parent 0d30528
commit 643061a
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Showing 7 changed files with 16 additions and 12 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -108,6 +108,9 @@ jobs:
 
   profile_download:
     name: nf-test with profiles needing entrez downloads
+    # Only run on PRs from branches of nf-core/metapep repository or on push if this is the nf-core dev branch (merged PRs)
+    # (GitHub secrets are not accessible for workflows from forks)
+    if: ${{ github.event.pull_request.head.repo.full_name == 'nf-core/metapep' || (github.event_name == 'push' && github.repository == 'nf-core/metapep') }}
     needs: define_nxf_versions
     runs-on: ubuntu-latest
     strategy:

diff --git a/nf-test.config b/nf-test.config
@@ -1,5 +1,3 @@
-config {
-
 config {
     // location for all nf-tests
     testsDir "tests"
@@ -15,6 +13,6 @@ config {
 
     // run all test with the defined docker profile from the main nextflow.config
     profile ""
-}
 
 }
+
diff --git a/tests/nextflow.config b/tests/nextflow.config
@@ -1 +1,4 @@
-// Impose same minimum Nextflow version as the pipeline for testing
+env {
+    NCBI_EMAIL = "$NCBI_EMAIL"
+    NCBI_KEY   = "$NCBI_KEY"
+    }
diff --git a/tests/pipeline/test_all.nf.test b/tests/pipeline/test_all.nf.test
@@ -10,8 +10,8 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                ncbi_email = "$NCBI_EMAIL"
-                ncbi_key = "$NCBI_KEY"
+                ncbi_email = "\$NCBI_EMAIL"
+                ncbi_key = "\$NCBI_KEY"
             }
         }
 

diff --git a/tests/pipeline/test_mouse.nf.test b/tests/pipeline/test_mouse.nf.test
@@ -10,8 +10,8 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                ncbi_email = "$NCBI_EMAIL"
-                ncbi_key = "$NCBI_KEY"
+                ncbi_email = "\$NCBI_EMAIL"
+                ncbi_key = "\$NCBI_KEY"
             }
         }
 

diff --git a/tests/pipeline/test_taxa_only.nf.test b/tests/pipeline/test_taxa_only.nf.test
@@ -10,8 +10,8 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                ncbi_email = "$NCBI_EMAIL"
-                ncbi_key = "$NCBI_KEY"
+                ncbi_email = "\$NCBI_EMAIL"
+                ncbi_key = "\$NCBI_KEY"
             }
         }
 

diff --git a/tests/pipeline/test_taxa_specific_assembly.nf.test b/tests/pipeline/test_taxa_specific_assembly.nf.test
@@ -10,8 +10,8 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                ncbi_email = "$NCBI_EMAIL"
-                ncbi_key = "$NCBI_KEY"
+                ncbi_email = "\$NCBI_EMAIL"
+                ncbi_key = "\$NCBI_KEY"
             }
         }